HEADER RECEPTOR 22-MAY-06 2CNJ TITLE NMR STUDIES ON THE INTERACTION OF INSULIN-GROWTH FACTOR II (IGF-II) TITLE 2 WITH IGF2R DOMAIN 11 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR; COMPND 3 CHAIN: D; COMPND 4 FRAGMENT: DOMAIN 11, RESIDUES 1508-1650; COMPND 5 SYNONYM: IGF2R DOMAIN 11, CI MAN-6-P RECEPTOR, CI-MPR, M6PR, INSULIN- COMPND 6 LIKE GROWTH FACTOR 2 RECEPTOR, INSULIN-LIKE GROWTH FACTOR II COMPND 7 RECEPTOR, IGF-II RECEPTOR, M6P/IGF2 RECEPTOR, M6P/IGF2R, 300 KDA COMPND 8 MANNOSE 6-PHOSPHATE RECEPTOR, MPR 300, MPR300, CD222 ANTIGEN; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET22 KEYWDS TRANSPORT, POLYMORPHISM, GLYCOPROTEIN, TRANSMEMBRANE, IGF2R, CANCER, KEYWDS 2 MEMBRANE, RECEPTOR, LYSOSOME, INSULIN-LIKE GROWTH FACTOR-II EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.WILLIAMS,S.PRINCE,O.ZACCHEO,A.B.HASSAN,J.CROSBY,M.CRUMP REVDAT 3 15-MAY-24 2CNJ 1 REMARK REVDAT 2 24-FEB-09 2CNJ 1 VERSN REVDAT 1 22-MAY-07 2CNJ 0 JRNL AUTH C.WILLIAMS,D.REZGUI,S.N.PRINCE,O.J.ZACCHEO,E.J.FOULSTONE, JRNL AUTH 2 B.E.FORBES,R.S.NORTON,J.CROSBY,A.B.HASSAN,M.P.CRUMP JRNL TITL STRUCTURAL INSIGHTS INTO THE INTERACTION OF INSULIN-LIKE JRNL TITL 2 GROWTH FACTOR 2 WITH IGF2R DOMAIN 11. JRNL REF STRUCTURE V. 15 1065 2007 JRNL REFN ISSN 0969-2126 JRNL PMID 17850746 JRNL DOI 10.1016/J.STR.2007.07.007 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- REMARK 3 KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE, REMARK 3 SIMONSON,WARREN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: WATER REFINED USING RECORRD SCIPTS IN REMARK 3 CNS. A.J.NEDERVEEN,J.F.DORELEIJERS,W.VRANKEN, Z.MILLER, REMARK 3 C.A.SPRONK, S.B.NABUURS, P.GUNTERT, M.LIVNY, J.L.MARKLEY, REMARK 3 M.NILGES, E.L.ULRICH, R.KAPTEIN AND A.M.BONVIN, PROTEINS. REMARK 3 RECOORD: A RECALCULATED COORDINATES DATABASE OF 500+ PROTEINS REMARK 3 FROM THE PDB USING RESTRAINTS FROM THE BIOMAGRESBANK. PROTEINS REMARK 3 59, 662-672. REMARK 4 REMARK 4 2CNJ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-MAY-06. REMARK 100 THE DEPOSITION ID IS D_1290028829. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298.0 REMARK 210 PH : 5.5 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1.0 ATM REMARK 210 SAMPLE CONTENTS : 5% D2O/ 95% H2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : HSQC; TOCSY; NOESY; HNCA; REMARK 210 HNCACB; CBCACONH; HCCH- TCOSY; REMARK 210 HNHA; HNBA; HNCO; HNCACO; HNCOCA REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY, NMRDRAW, NMRPIPE, CNS REMARK 210 METHOD USED : WATER REFINED IN CNS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST ENERGY, LEAST VIOLATION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY ON UNLABELLED, 15N AND 13C, 15N-LABELED DOMAIN 11. REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 400 REMARK 400 COMPOUND REMARK 400 PROMOTES THE TRANSPORT OF PHOSPHORYLATED LYSOSOMAL ENZYMES. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 MET D 1508 REMARK 465 LYS D 1509 REMARK 465 HIS D 1654 REMARK 465 HIS D 1655 REMARK 465 HIS D 1656 REMARK 465 HIS D 1657 REMARK 465 HIS D 1658 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-20 REMARK 470 RES CSSEQI ATOMS REMARK 470 HIS D1653 CA C O CB CG ND1 CD2 REMARK 470 HIS D1653 CE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 H PHE D 1538 O MET D 1550 1.56 REMARK 500 OD2 ASP D 1630 HG1 THR D 1633 1.58 REMARK 500 O SER D 1551 HH TYR D 1592 1.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 2 CYS D1634 CA CYS D1634 CB -0.086 REMARK 500 5 CYS D1634 CA CYS D1634 CB -0.078 REMARK 500 6 CYS D1634 CA CYS D1634 CB -0.080 REMARK 500 7 CYS D1634 CA CYS D1634 CB -0.089 REMARK 500 8 CYS D1634 CA CYS D1634 CB -0.083 REMARK 500 9 CYS D1634 CA CYS D1634 CB -0.087 REMARK 500 12 CYS D1634 CA CYS D1634 CB -0.082 REMARK 500 13 CYS D1634 CA CYS D1634 CB -0.080 REMARK 500 14 CYS D1634 C THR D1635 N -0.143 REMARK 500 15 CYS D1634 CA CYS D1634 CB -0.079 REMARK 500 16 CYS D1634 CA CYS D1634 CB -0.080 REMARK 500 18 CYS D1634 CA CYS D1634 CB -0.096 REMARK 500 19 CYS D1634 CA CYS D1634 CB -0.085 REMARK 500 20 CYS D1634 CA CYS D1634 CB -0.087 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 ASN D1511 107.09 72.45 REMARK 500 1 GLU D1512 -174.26 76.39 REMARK 500 1 HIS D1513 -76.60 -142.32 REMARK 500 1 ASP D1515 164.32 75.50 REMARK 500 1 SER D1543 -141.43 53.75 REMARK 500 1 CYS D1553 -31.57 70.09 REMARK 500 1 PRO D1561 106.73 -50.61 REMARK 500 1 LYS D1601 -158.51 -149.39 REMARK 500 1 ASN D1622 69.44 76.43 REMARK 500 1 THR D1633 19.96 -145.14 REMARK 500 1 GLU D1647 -37.68 166.52 REMARK 500 2 HIS D1513 -78.27 -131.97 REMARK 500 2 ASP D1515 162.30 73.44 REMARK 500 2 THR D1523 -38.39 -130.17 REMARK 500 2 SER D1543 -149.42 51.51 REMARK 500 2 PRO D1561 108.24 -51.51 REMARK 500 2 CYS D1614 95.01 -68.62 REMARK 500 2 ALA D1618 177.25 -54.67 REMARK 500 2 ASN D1622 77.24 61.28 REMARK 500 2 GLU D1647 -44.81 -176.39 REMARK 500 2 GLN D1648 -67.00 -100.02 REMARK 500 2 GLU D1652 -87.71 -109.96 REMARK 500 3 ASN D1511 79.54 -106.07 REMARK 500 3 HIS D1513 -87.88 -140.97 REMARK 500 3 ASP D1515 162.13 70.86 REMARK 500 3 CYS D1516 3.38 59.40 REMARK 500 3 THR D1523 -33.60 -138.59 REMARK 500 3 SER D1543 -135.86 54.90 REMARK 500 3 CYS D1553 19.51 55.18 REMARK 500 3 PRO D1561 105.58 -52.35 REMARK 500 3 GLN D1586 -4.05 71.16 REMARK 500 3 LYS D1601 -162.15 -160.25 REMARK 500 3 ASN D1622 60.97 79.92 REMARK 500 3 THR D1633 -47.97 -136.16 REMARK 500 3 CYS D1634 1.20 149.75 REMARK 500 3 GLU D1647 -30.67 168.22 REMARK 500 3 GLU D1652 -108.01 -108.23 REMARK 500 4 ASN D1511 -72.39 -87.26 REMARK 500 4 HIS D1513 -96.77 -137.96 REMARK 500 4 ASP D1515 168.79 73.17 REMARK 500 4 CYS D1516 7.55 52.24 REMARK 500 4 SER D1543 -152.97 58.21 REMARK 500 4 CYS D1553 16.08 56.23 REMARK 500 4 PRO D1561 105.67 -56.76 REMARK 500 4 LYS D1601 -162.38 -128.83 REMARK 500 4 ASN D1622 63.48 74.87 REMARK 500 4 GLU D1647 -36.48 174.00 REMARK 500 4 GLU D1652 -67.25 -95.08 REMARK 500 5 HIS D1513 -80.46 -125.74 REMARK 500 5 ASP D1515 161.71 72.45 REMARK 500 REMARK 500 THIS ENTRY HAS 223 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 8 ARG D1623 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1E6F RELATED DB: PDB REMARK 900 HUMAN MIR-RECEPTOR, REPEAT 11 REMARK 900 RELATED ID: 1GP0 RELATED DB: PDB REMARK 900 STRUCTURE OF A FUNCTIONAL IGF2R FRAGMENT DETERMINED FROM ANOMALOUS REMARK 900 SCATTERING OF SULPHUR REMARK 900 RELATED ID: 1GP3 RELATED DB: PDB REMARK 900 STRUCTURE OF A FUNCTIONAL IGF2R FRAGMENT DETERMINED FROM ANOMALOUS REMARK 900 SCATTERING OF SULPHUR REMARK 900 RELATED ID: 1GQB RELATED DB: PDB REMARK 900 HUMAN MIR-RECEPTOR, REPEAT 11 REMARK 900 RELATED ID: 1JPL RELATED DB: PDB REMARK 900 GGA3 VHS DOMAIN COMPLEXED WITH C-TERMINAL PEPTIDE FROMCATION- REMARK 900 INDEPENDENT MANNOSE 6- PHOSPHATE RECEPTOR REMARK 900 RELATED ID: 1JWG RELATED DB: PDB REMARK 900 VHS DOMAIN OF HUMAN GGA1 COMPLEXED WITH CATION-INDEPENDENTM6PR C- REMARK 900 TERMINAL PEPTIDE REMARK 900 RELATED ID: 1LF8 RELATED DB: PDB REMARK 900 COMPLEX OF GGA3-VHS DOMAIN AND CI-MPR C -TERMINALPHOSPHOPEPTIDE DBREF 2CNJ D 1508 1650 UNP P11717 MPRI_HUMAN 1508 1650 DBREF 2CNJ D 1651 1658 PDB 2CNJ 2CNJ 1651 1658 SEQRES 1 D 151 MET LYS SER ASN GLU HIS ASP ASP CYS GLN VAL THR ASN SEQRES 2 D 151 PRO SER THR GLY HIS LEU PHE ASP LEU SER SER LEU SER SEQRES 3 D 151 GLY ARG ALA GLY PHE THR ALA ALA TYR SER GLU LYS GLY SEQRES 4 D 151 LEU VAL TYR MET SER ILE CYS GLY GLU ASN GLU ASN CYS SEQRES 5 D 151 PRO PRO GLY VAL GLY ALA CYS PHE GLY GLN THR ARG ILE SEQRES 6 D 151 SER VAL GLY LYS ALA ASN LYS ARG LEU ARG TYR VAL ASP SEQRES 7 D 151 GLN VAL LEU GLN LEU VAL TYR LYS ASP GLY SER PRO CYS SEQRES 8 D 151 PRO SER LYS SER GLY LEU SER TYR LYS SER VAL ILE SER SEQRES 9 D 151 PHE VAL CYS ARG PRO GLU ALA GLY PRO THR ASN ARG PRO SEQRES 10 D 151 MET LEU ILE SER LEU ASP LYS GLN THR CYS THR LEU PHE SEQRES 11 D 151 PHE SER TRP HIS THR PRO LEU ALA CYS GLU GLN ALA THR SEQRES 12 D 151 LYS GLU HIS HIS HIS HIS HIS HIS HELIX 1 1 PRO D 1643 CYS D 1646 5 4 SHEET 1 DA 2 GLN D1517 THR D1519 0 SHEET 2 DA 2 LEU D1526 ASP D1528 -1 O PHE D1527 N VAL D1518 SHEET 1 DB 4 PHE D1538 TYR D1542 0 SHEET 2 DB 4 GLY D1546 MET D1550 -1 O GLY D1546 N TYR D1542 SHEET 3 DB 4 VAL D1563 PHE D1567 -1 O CYS D1566 N TYR D1549 SHEET 4 DB 4 GLY D1575 LYS D1576 -1 O GLY D1575 N ALA D1565 SHEET 1 DC 5 ARG D1582 VAL D1584 0 SHEET 2 DC 5 VAL D1587 LEU D1590 -1 O VAL D1587 N VAL D1584 SHEET 3 DC 5 LYS D1607 CYS D1614 -1 O ILE D1610 N LEU D1590 SHEET 4 DC 5 THR D1635 THR D1642 1 O LEU D1636 N VAL D1609 SHEET 5 DC 5 MET D1625 ASP D1630 -1 O MET D1625 N SER D1639 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1